Multiple sequence alignment - TraesCS1A01G165900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G165900 chr1A 100.000 3934 0 0 1 3934 298616553 298612620 0.000000e+00 7265.0
1 TraesCS1A01G165900 chr1A 88.013 634 38 8 1 598 395487574 395486943 0.000000e+00 715.0
2 TraesCS1A01G165900 chr1A 90.223 358 27 4 638 988 395486875 395486519 9.960000e-126 460.0
3 TraesCS1A01G165900 chr1A 93.684 190 9 1 803 989 298620933 298621122 8.320000e-72 281.0
4 TraesCS1A01G165900 chr1A 90.226 133 9 2 794 922 395493034 395493166 1.880000e-38 171.0
5 TraesCS1A01G165900 chr1D 96.789 2118 55 8 990 3100 248984961 248987072 0.000000e+00 3522.0
6 TraesCS1A01G165900 chr1D 89.628 887 56 13 3059 3934 248987071 248987932 0.000000e+00 1096.0
7 TraesCS1A01G165900 chr1D 83.286 706 84 14 3223 3924 198924605 198925280 1.550000e-173 619.0
8 TraesCS1A01G165900 chr1D 90.419 167 16 0 1205 1371 419920061 419919895 1.840000e-53 220.0
9 TraesCS1A01G165900 chr1D 86.979 192 15 7 803 990 138970073 138970258 1.430000e-49 207.0
10 TraesCS1A01G165900 chr1D 88.034 117 14 0 1 117 138968947 138968831 5.300000e-29 139.0
11 TraesCS1A01G165900 chr1D 72.521 353 75 18 656 993 138968562 138968217 1.160000e-15 95.3
12 TraesCS1A01G165900 chr1D 95.652 46 2 0 1205 1250 15166142 15166187 1.520000e-09 75.0
13 TraesCS1A01G165900 chr1D 95.652 46 2 0 1205 1250 29389934 29389979 1.520000e-09 75.0
14 TraesCS1A01G165900 chr1B 93.077 1979 111 17 990 2957 329490703 329488740 0.000000e+00 2872.0
15 TraesCS1A01G165900 chr2A 99.292 989 6 1 1 989 58553308 58552321 0.000000e+00 1786.0
16 TraesCS1A01G165900 chr7B 99.479 959 5 0 1 959 20889194 20890152 0.000000e+00 1744.0
17 TraesCS1A01G165900 chr7B 93.194 191 10 1 803 990 20884859 20884669 1.080000e-70 278.0
18 TraesCS1A01G165900 chr7B 92.258 155 10 2 2153 2306 453623443 453623290 6.620000e-53 219.0
19 TraesCS1A01G165900 chr7B 83.146 89 9 4 3131 3214 742340464 742340377 4.220000e-10 76.8
20 TraesCS1A01G165900 chr7B 80.000 100 10 6 2945 3044 442375870 442375781 9.120000e-07 65.8
21 TraesCS1A01G165900 chr3B 97.643 594 11 3 1 593 754456637 754457228 0.000000e+00 1016.0
22 TraesCS1A01G165900 chr3B 97.427 583 11 3 1 582 703880325 703880904 0.000000e+00 990.0
23 TraesCS1A01G165900 chr3B 89.881 336 6 6 657 989 754457529 754457839 1.320000e-109 407.0
24 TraesCS1A01G165900 chr3B 93.939 231 11 1 762 989 703881738 703881968 2.910000e-91 346.0
25 TraesCS1A01G165900 chr3B 92.105 190 11 2 803 989 703857789 703857601 8.380000e-67 265.0
26 TraesCS1A01G165900 chr3B 92.063 189 12 1 803 988 754452110 754451922 3.010000e-66 263.0
27 TraesCS1A01G165900 chr3B 90.526 190 18 0 1205 1394 597010202 597010013 6.530000e-63 252.0
28 TraesCS1A01G165900 chr3B 97.222 108 3 0 659 766 703881255 703881362 2.410000e-42 183.0
29 TraesCS1A01G165900 chr4A 81.250 1008 127 32 2950 3924 84951883 84952861 0.000000e+00 758.0
30 TraesCS1A01G165900 chr5B 90.698 516 30 4 1 500 232563261 232562748 0.000000e+00 671.0
31 TraesCS1A01G165900 chr5B 91.944 360 23 3 638 991 232562605 232562246 2.110000e-137 499.0
32 TraesCS1A01G165900 chr5B 74.622 331 40 20 1 305 676267912 676267600 5.380000e-19 106.0
33 TraesCS1A01G165900 chr5A 78.482 1041 149 45 1 990 423035441 423034425 2.600000e-171 612.0
34 TraesCS1A01G165900 chr5A 77.588 1053 152 39 1 991 662625024 662623994 9.550000e-156 560.0
35 TraesCS1A01G165900 chr5A 95.122 41 1 1 2947 2987 14132427 14132388 3.280000e-06 63.9
36 TraesCS1A01G165900 chr2D 80.043 927 98 33 3018 3899 207240576 207239692 1.210000e-169 606.0
37 TraesCS1A01G165900 chr2D 85.409 562 73 6 3368 3921 569114042 569114602 3.410000e-160 575.0
38 TraesCS1A01G165900 chr2D 83.808 562 68 9 3224 3785 490116838 490116300 2.710000e-141 512.0
39 TraesCS1A01G165900 chr2D 91.613 155 11 2 2153 2306 88290208 88290055 3.080000e-51 213.0
40 TraesCS1A01G165900 chr2D 95.122 41 0 1 2949 2989 261976647 261976609 3.280000e-06 63.9
41 TraesCS1A01G165900 chr6B 80.788 838 105 27 2955 3770 670031305 670030502 4.350000e-169 604.0
42 TraesCS1A01G165900 chr6B 86.325 117 16 0 1 117 493510843 493510727 1.150000e-25 128.0
43 TraesCS1A01G165900 chr3A 77.905 1050 146 44 1 989 142908912 142907888 3.410000e-160 575.0
44 TraesCS1A01G165900 chr3A 77.579 950 125 47 2997 3924 26728263 26729146 9.820000e-136 494.0
45 TraesCS1A01G165900 chr3A 90.909 165 10 5 2154 2316 466791159 466790998 2.380000e-52 217.0
46 TraesCS1A01G165900 chr3A 97.368 38 0 1 2950 2987 709096104 709096068 3.280000e-06 63.9
47 TraesCS1A01G165900 chr6D 84.804 408 50 2 3370 3774 444890460 444890858 2.200000e-107 399.0
48 TraesCS1A01G165900 chr6D 76.399 572 120 8 3353 3915 324555508 324556073 1.070000e-75 294.0
49 TraesCS1A01G165900 chr6D 81.564 358 56 7 3571 3924 458200812 458200461 1.790000e-73 287.0
50 TraesCS1A01G165900 chr6D 81.440 361 55 8 3567 3924 458231354 458231003 6.430000e-73 285.0
51 TraesCS1A01G165900 chr6D 81.250 240 40 5 3687 3924 458300383 458300147 5.190000e-44 189.0
52 TraesCS1A01G165900 chr6D 95.652 46 2 0 1205 1250 78589819 78589864 1.520000e-09 75.0
53 TraesCS1A01G165900 chr2B 80.830 506 74 10 3365 3866 84440336 84440822 3.710000e-100 375.0
54 TraesCS1A01G165900 chr2B 89.691 194 20 0 1205 1398 702215598 702215405 8.440000e-62 248.0
55 TraesCS1A01G165900 chr2B 90.625 160 12 3 2153 2310 141562323 141562165 3.980000e-50 209.0
56 TraesCS1A01G165900 chr2B 92.105 76 5 1 3850 3924 84298569 84298644 5.380000e-19 106.0
57 TraesCS1A01G165900 chr7D 93.048 187 13 0 1212 1398 322287118 322286932 1.390000e-69 274.0
58 TraesCS1A01G165900 chr7D 92.258 155 10 2 2153 2306 436961948 436961795 6.620000e-53 219.0
59 TraesCS1A01G165900 chr7D 75.465 269 35 21 3131 3371 608210131 608209866 6.950000e-18 102.0
60 TraesCS1A01G165900 chr7D 94.545 55 3 0 1259 1313 158430719 158430665 7.000000e-13 86.1
61 TraesCS1A01G165900 chr7D 92.308 52 4 0 1262 1313 366417106 366417055 1.520000e-09 75.0
62 TraesCS1A01G165900 chr7D 80.412 97 16 3 2950 3045 608210326 608210232 1.960000e-08 71.3
63 TraesCS1A01G165900 chr5D 91.124 169 15 0 1205 1373 430257926 430257758 3.060000e-56 230.0
64 TraesCS1A01G165900 chr5D 95.652 46 2 0 1205 1250 6150292 6150337 1.520000e-09 75.0
65 TraesCS1A01G165900 chr7A 91.613 155 11 2 2153 2306 486930093 486929940 3.080000e-51 213.0
66 TraesCS1A01G165900 chr3D 89.820 167 12 5 2153 2316 347585387 347585223 3.980000e-50 209.0
67 TraesCS1A01G165900 chr3D 87.255 102 13 0 1 102 596660440 596660541 2.480000e-22 117.0
68 TraesCS1A01G165900 chr4D 95.652 46 2 0 1205 1250 76301759 76301714 1.520000e-09 75.0
69 TraesCS1A01G165900 chrUn 91.304 46 3 1 2941 2986 58513437 58513481 1.180000e-05 62.1
70 TraesCS1A01G165900 chrUn 91.304 46 3 1 2941 2986 59594004 59593960 1.180000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G165900 chr1A 298612620 298616553 3933 True 7265.000000 7265 100.0000 1 3934 1 chr1A.!!$R1 3933
1 TraesCS1A01G165900 chr1A 395486519 395487574 1055 True 587.500000 715 89.1180 1 988 2 chr1A.!!$R2 987
2 TraesCS1A01G165900 chr1D 248984961 248987932 2971 False 2309.000000 3522 93.2085 990 3934 2 chr1D.!!$F5 2944
3 TraesCS1A01G165900 chr1D 198924605 198925280 675 False 619.000000 619 83.2860 3223 3924 1 chr1D.!!$F4 701
4 TraesCS1A01G165900 chr1B 329488740 329490703 1963 True 2872.000000 2872 93.0770 990 2957 1 chr1B.!!$R1 1967
5 TraesCS1A01G165900 chr2A 58552321 58553308 987 True 1786.000000 1786 99.2920 1 989 1 chr2A.!!$R1 988
6 TraesCS1A01G165900 chr7B 20889194 20890152 958 False 1744.000000 1744 99.4790 1 959 1 chr7B.!!$F1 958
7 TraesCS1A01G165900 chr3B 754456637 754457839 1202 False 711.500000 1016 93.7620 1 989 2 chr3B.!!$F2 988
8 TraesCS1A01G165900 chr3B 703880325 703881968 1643 False 506.333333 990 96.1960 1 989 3 chr3B.!!$F1 988
9 TraesCS1A01G165900 chr4A 84951883 84952861 978 False 758.000000 758 81.2500 2950 3924 1 chr4A.!!$F1 974
10 TraesCS1A01G165900 chr5B 232562246 232563261 1015 True 585.000000 671 91.3210 1 991 2 chr5B.!!$R2 990
11 TraesCS1A01G165900 chr5A 423034425 423035441 1016 True 612.000000 612 78.4820 1 990 1 chr5A.!!$R2 989
12 TraesCS1A01G165900 chr5A 662623994 662625024 1030 True 560.000000 560 77.5880 1 991 1 chr5A.!!$R3 990
13 TraesCS1A01G165900 chr2D 207239692 207240576 884 True 606.000000 606 80.0430 3018 3899 1 chr2D.!!$R2 881
14 TraesCS1A01G165900 chr2D 569114042 569114602 560 False 575.000000 575 85.4090 3368 3921 1 chr2D.!!$F1 553
15 TraesCS1A01G165900 chr2D 490116300 490116838 538 True 512.000000 512 83.8080 3224 3785 1 chr2D.!!$R4 561
16 TraesCS1A01G165900 chr6B 670030502 670031305 803 True 604.000000 604 80.7880 2955 3770 1 chr6B.!!$R2 815
17 TraesCS1A01G165900 chr3A 142907888 142908912 1024 True 575.000000 575 77.9050 1 989 1 chr3A.!!$R1 988
18 TraesCS1A01G165900 chr3A 26728263 26729146 883 False 494.000000 494 77.5790 2997 3924 1 chr3A.!!$F1 927
19 TraesCS1A01G165900 chr6D 324555508 324556073 565 False 294.000000 294 76.3990 3353 3915 1 chr6D.!!$F2 562

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1071 1871 2.193536 GGAGAGGAGAGAGAGCCGC 61.194 68.421 0.0 0.0 0.0 6.53 F
1189 1989 0.036306 TCCCTCGCTTGGTTTCTTCC 59.964 55.000 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2855 3665 3.220110 CATATCTCTGCAGGGCACAAAT 58.780 45.455 15.13 1.48 33.79 2.32 R
3186 4054 0.620556 ACAACCTCCTCGGCATGAAT 59.379 50.000 0.00 0.00 35.61 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1071 1871 2.193536 GGAGAGGAGAGAGAGCCGC 61.194 68.421 0.00 0.00 0.00 6.53
1074 1874 2.441901 AGGAGAGAGAGCCGCTGG 60.442 66.667 0.00 0.00 0.00 4.85
1155 1955 2.103263 GTCCATCGGCTCCTCTAACATT 59.897 50.000 0.00 0.00 0.00 2.71
1189 1989 0.036306 TCCCTCGCTTGGTTTCTTCC 59.964 55.000 0.00 0.00 0.00 3.46
1190 1990 0.960861 CCCTCGCTTGGTTTCTTCCC 60.961 60.000 0.00 0.00 0.00 3.97
1210 2010 2.363292 CTGCCCATCCATCCTTCCCC 62.363 65.000 0.00 0.00 0.00 4.81
1211 2011 2.839098 CCCATCCATCCTTCCCCG 59.161 66.667 0.00 0.00 0.00 5.73
1214 2014 3.178611 ATCCATCCTTCCCCGCCC 61.179 66.667 0.00 0.00 0.00 6.13
1215 2015 4.750695 TCCATCCTTCCCCGCCCA 62.751 66.667 0.00 0.00 0.00 5.36
1254 2058 0.958091 ATGCTTTGTTGCCTTGCGTA 59.042 45.000 0.00 0.00 0.00 4.42
1255 2059 0.958091 TGCTTTGTTGCCTTGCGTAT 59.042 45.000 0.00 0.00 0.00 3.06
1274 2078 0.884259 TGCCTGATGGTCGTGTGTTG 60.884 55.000 0.00 0.00 35.27 3.33
1352 2156 1.294780 CAGGAGCAGGTCTGTGTCC 59.705 63.158 11.28 11.28 36.60 4.02
1413 2217 1.204467 CCCATTTTCACCCAATCCGTG 59.796 52.381 0.00 0.00 0.00 4.94
1434 2238 7.884354 TCCGTGTGTTAGTTTTAGGGATAATTT 59.116 33.333 0.00 0.00 0.00 1.82
1452 2256 7.435192 GGATAATTTTGTTAGTTGTAGCATGGC 59.565 37.037 0.00 0.00 0.00 4.40
1458 2262 0.987294 AGTTGTAGCATGGCACTCCT 59.013 50.000 0.00 0.00 0.00 3.69
1462 2266 1.905894 TGTAGCATGGCACTCCTAACA 59.094 47.619 0.00 0.00 0.00 2.41
1557 2363 5.492895 TGTGTTTCTCCAAGTGTTGTAAGA 58.507 37.500 0.00 0.00 0.00 2.10
1588 2394 2.353889 CTGGTCTTTGAGATCATTGCGG 59.646 50.000 0.00 0.00 34.36 5.69
1891 2700 7.873505 GCTTGTTACTTATAGTTGCCTAGCTAT 59.126 37.037 0.00 0.00 35.02 2.97
2216 3026 8.965986 TTTTCTGAATCGGATGTATATAGACG 57.034 34.615 0.00 0.00 0.00 4.18
2241 3051 8.308320 CGTGTTTTAATGTGTTTGTTTACTCAC 58.692 33.333 0.00 0.00 0.00 3.51
2877 3687 0.471191 TGTGCCCTGCAGAGATATGG 59.529 55.000 17.39 7.76 40.08 2.74
2994 3807 2.742372 CAACGGCGCTTGTAGGCT 60.742 61.111 6.90 0.00 0.00 4.58
3184 4052 9.631452 GTAGATACAAACGTAAAACTACTCCTT 57.369 33.333 0.00 0.00 30.45 3.36
3216 4086 3.438087 CGAGGAGGTTGTAGAAGACGTTA 59.562 47.826 0.00 0.00 0.00 3.18
3219 4089 5.963594 AGGAGGTTGTAGAAGACGTTATTC 58.036 41.667 6.39 6.39 0.00 1.75
3294 4200 2.045926 GGATTGCCGCTGTGGACT 60.046 61.111 12.29 0.00 42.00 3.85
3347 4253 1.109609 TCAGAGAGCATGATGACGCT 58.890 50.000 0.00 0.00 42.42 5.07
3348 4254 1.202382 TCAGAGAGCATGATGACGCTG 60.202 52.381 13.79 13.79 38.99 5.18
3349 4255 0.530211 AGAGAGCATGATGACGCTGC 60.530 55.000 0.00 0.00 38.99 5.25
3350 4256 1.497223 GAGAGCATGATGACGCTGCC 61.497 60.000 0.00 0.00 38.99 4.85
3351 4257 2.515523 AGCATGATGACGCTGCCC 60.516 61.111 0.00 0.00 37.02 5.36
3352 4258 2.515523 GCATGATGACGCTGCCCT 60.516 61.111 0.00 0.00 0.00 5.19
3353 4259 2.541120 GCATGATGACGCTGCCCTC 61.541 63.158 0.00 0.00 0.00 4.30
3354 4260 2.107750 ATGATGACGCTGCCCTCG 59.892 61.111 0.00 0.00 0.00 4.63
3355 4261 2.725312 ATGATGACGCTGCCCTCGT 61.725 57.895 0.00 0.00 43.49 4.18
3499 4406 4.778143 GTCGGCGGCCATGTCCTT 62.778 66.667 20.71 0.00 0.00 3.36
3560 4473 1.672030 CTTGACCAGGCGCATGTGA 60.672 57.895 21.79 0.67 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1118 1918 1.010574 GACGACATCGCCTCTCTCG 60.011 63.158 0.14 0.00 44.43 4.04
1155 1955 3.319198 GGACGGACCTGGAAGCCA 61.319 66.667 0.00 0.00 35.41 4.75
1189 1989 1.152368 GAAGGATGGATGGGCAGGG 59.848 63.158 0.00 0.00 0.00 4.45
1190 1990 1.152368 GGAAGGATGGATGGGCAGG 59.848 63.158 0.00 0.00 0.00 4.85
1214 2014 0.034477 AAACCCTAATCCCCAGCGTG 60.034 55.000 0.00 0.00 0.00 5.34
1215 2015 0.034477 CAAACCCTAATCCCCAGCGT 60.034 55.000 0.00 0.00 0.00 5.07
1219 2023 1.929494 AGCATCAAACCCTAATCCCCA 59.071 47.619 0.00 0.00 0.00 4.96
1221 2025 3.769300 ACAAAGCATCAAACCCTAATCCC 59.231 43.478 0.00 0.00 0.00 3.85
1254 2058 0.036732 AACACACGACCATCAGGCAT 59.963 50.000 0.00 0.00 39.06 4.40
1255 2059 0.884259 CAACACACGACCATCAGGCA 60.884 55.000 0.00 0.00 39.06 4.75
1274 2078 2.337532 CAGCTGCAGCAACCCAAC 59.662 61.111 38.24 8.57 45.16 3.77
1346 2150 6.498651 AGAAGAGAAAAGAGAATAGGGACACA 59.501 38.462 0.00 0.00 0.00 3.72
1352 2156 5.452636 CGGGGAGAAGAGAAAAGAGAATAGG 60.453 48.000 0.00 0.00 0.00 2.57
1434 2238 3.750371 AGTGCCATGCTACAACTAACAA 58.250 40.909 0.00 0.00 0.00 2.83
1452 2256 2.492484 ACTAAGCCTCGTGTTAGGAGTG 59.508 50.000 0.00 0.00 39.15 3.51
1458 2262 3.428532 AGGAGAACTAAGCCTCGTGTTA 58.571 45.455 0.00 0.00 0.00 2.41
1462 2266 2.249139 ACAAGGAGAACTAAGCCTCGT 58.751 47.619 0.00 0.00 0.00 4.18
1557 2363 8.367660 TGATCTCAAAGACCAGTAATAAGACT 57.632 34.615 0.00 0.00 0.00 3.24
1588 2394 8.218338 AGTCCACAATATGAGACAATTTGATC 57.782 34.615 2.79 1.79 33.36 2.92
1891 2700 7.942341 AGTACACAAACAGAAATAATCCAGGAA 59.058 33.333 0.00 0.00 0.00 3.36
2216 3026 9.349145 AGTGAGTAAACAAACACATTAAAACAC 57.651 29.630 0.00 0.00 35.97 3.32
2241 3051 8.797350 TCAATATGGCTACATATGGATTGAAG 57.203 34.615 7.80 0.00 46.83 3.02
2855 3665 3.220110 CATATCTCTGCAGGGCACAAAT 58.780 45.455 15.13 1.48 33.79 2.32
2877 3687 6.579491 AAGAACGTCTGTTACAAGTTACAC 57.421 37.500 0.00 0.00 38.78 2.90
2994 3807 3.275999 GCCCCAAGAGACGCTATTTTTA 58.724 45.455 0.00 0.00 0.00 1.52
3057 3870 3.469863 ATGCCGTTGTGGTCGTGGT 62.470 57.895 0.00 0.00 41.21 4.16
3184 4052 2.238646 ACAACCTCCTCGGCATGAATTA 59.761 45.455 0.00 0.00 35.61 1.40
3185 4053 1.004745 ACAACCTCCTCGGCATGAATT 59.995 47.619 0.00 0.00 35.61 2.17
3186 4054 0.620556 ACAACCTCCTCGGCATGAAT 59.379 50.000 0.00 0.00 35.61 2.57
3499 4406 1.672737 CCGTAGTGAAGCATGAGCACA 60.673 52.381 13.20 0.00 45.49 4.57
3560 4473 2.685380 CCTTCCCCTCTCTGCGGT 60.685 66.667 0.00 0.00 0.00 5.68
3636 4549 4.200283 GCCCGAGTCGCAGGAGAG 62.200 72.222 7.12 0.00 0.00 3.20
3702 4616 3.745803 GCCGTCCTCGTCGTCCTT 61.746 66.667 0.00 0.00 35.01 3.36
3818 4749 2.992114 ACTCTCCTCGCCGTGCTT 60.992 61.111 0.00 0.00 0.00 3.91


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.